LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
  using 1 OpenMP thread(s) per MPI task
# Initialization
units           metal
boundary        p p p
atom_style      full
processors      * * 1     # domain decomposition over x and y

# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data       Bi_gr_AB_stack_2L_noH_300K.data
  orthogonal box = (0 0 0) to (42.6 41.8117 100)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  1360 atoms
  reading velocities ...
  1360 velocities
  0 = max # of 1-2 neighbors
  0 = max # of 1-3 neighbors
  0 = max # of 1-4 neighbors
  1 = max # of special neighbors
  special bonds CPU = 0.000353813 secs
  read_data CPU = 0.0043292 secs
mass            1 12.0107   # carbon mass (g/mole) | membrane
mass            2 12.0107   # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane  type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate

######################## Potential defition ########################
pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0
####################################################################
pair_coeff  * * rebo                     CH.rebo      NULL C  # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff  * * kolmogorov/crespi/full   CC.KC-full     C    C  # long range
####################################################################
# Neighbor update settings
neighbor        2.0 bin
neigh_modify    every 1
neigh_modify    delay 0
neigh_modify    check yes

# calculate the COM
variable        adsxcom equal xcm(adsorbate,x)
variable        adsycom equal xcm(adsorbate,y)
variable        adszcom equal xcm(adsorbate,z)
variable        adsvxcom equal vcm(adsorbate,x)
variable        adsvycom equal vcm(adsorbate,y)
variable        adsvzcom equal vcm(adsorbate,z)

#### Simulation settings ####
timestep  0.001
fix       subf membrane setforce 0.0 0.0 0.0
fix       thermostat all nve

compute   0 all pair rebo
compute   1 all pair kolmogorov/crespi/full
variable  REBO     equal c_0
variable  KC       equal c_1

############################

# Output
thermo          100
thermo_style    custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify   line one format float %.10f
thermo_modify   flush yes norm no lost warn #ignore

#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes

###### Run molecular dynamics ######
run 1000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 18
  ghost atom cutoff = 18
  binsize = 9, bins = 5 5 12
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair rebo, perpetual, skip from (2)
      attributes: full, newton on, ghost
      pair build: skip/ghost
      stencil: none
      bin: none
  (2) pair kolmogorov/crespi/full, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
       0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 
     100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015 
     200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578 
     300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907 
     400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393292 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497 
     500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 
     600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092 
     700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565 
     800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926 
     900 -5025.3984547937 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640 
    1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 
Loop time of 103.724 on 1 procs for 1000 steps with 1360 atoms

Performance: 0.833 ns/day, 28.812 hours/ns, 9.641 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 103.59     | 103.59     | 103.59     |   0.0 | 99.87
Bond    | 0.00022388 | 0.00022388 | 0.00022388 |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.082476   | 0.082476   | 0.082476   |   0.0 |  0.08
Output  | 0.0010884  | 0.0010884  | 0.0010884  |   0.0 |  0.00
Modify  | 0.032938   | 0.032938   | 0.032938   |   0.0 |  0.03
Other   |            | 0.01749    |            |       |  0.02

Nlocal:    1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  265206 ave 265206 max 265206 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:43
